From d5f1f28686fb09f9d78a48ab0582e3343494bde0 Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Wed, 26 Jun 2024 14:00:11 -0400 Subject: [PATCH 1/2] update ids --- v03_pipeline/lib/annotations/enums.py | 7 ------- v03_pipeline/lib/annotations/snv_indel_test.py | 13 +++++++------ ...riant_annotations_table_with_new_samples_test.py | 10 +++++----- 3 files changed, 12 insertions(+), 18 deletions(-) diff --git a/v03_pipeline/lib/annotations/enums.py b/v03_pipeline/lib/annotations/enums.py index 8b469cda9..16033214f 100644 --- a/v03_pipeline/lib/annotations/enums.py +++ b/v03_pipeline/lib/annotations/enums.py @@ -48,7 +48,6 @@ 'ambiguous_orf', 'sense_intronic', 'sense_overlapping', - 'antisense/antisense_RNA', 'antisense', 'known_ncrna', 'pseudogene', @@ -64,12 +63,9 @@ 'unprocessed_pseudogene', 'artifact', 'lincRNA', - 'lincrna', 'macro_lncRNA', '3prime_overlapping_ncRNA', 'disrupted_domain', - 'vaultRNA/vault_RNA', - 'vaultRNA', 'vault_RNA', 'bidirectional_promoter_lncRNA', '3prime_overlapping_ncrna', @@ -91,9 +87,6 @@ 'frameshift_variant', 'stop_lost', 'start_lost', - 'transcript_amplification', - 'feature_elongation', - 'feature_truncation', 'inframe_insertion', 'inframe_deletion', 'missense_variant', diff --git a/v03_pipeline/lib/annotations/snv_indel_test.py b/v03_pipeline/lib/annotations/snv_indel_test.py index 10f6d369f..00b411245 100644 --- a/v03_pipeline/lib/annotations/snv_indel_test.py +++ b/v03_pipeline/lib/annotations/snv_indel_test.py @@ -119,6 +119,7 @@ def test_sorted_transcript_consequences_37( ht, ), ) + print(ht.sorted_transcript_consequences.collect()) self.assertCountEqual( ht.sorted_transcript_consequences.collect(), [ @@ -132,7 +133,7 @@ def test_sorted_transcript_consequences_37( hgvsp='ENSP00000317992.6:p.Ser556Leu', transcript_id='ENST00000327044', biotype_id=39, - consequence_term_ids=[12], + consequence_term_ids=[9], is_lof_nagnag=None, lof_filter_ids=[0, 1], ), @@ -145,7 +146,7 @@ def test_sorted_transcript_consequences_37( hgvsp=None, transcript_id='ENST00000477976', biotype_id=38, - consequence_term_ids=[26, 29], + consequence_term_ids=[23, 26], is_lof_nagnag=None, lof_filter_ids=None, ), @@ -158,7 +159,7 @@ def test_sorted_transcript_consequences_37( hgvsp=None, transcript_id='ENST00000483767', biotype_id=38, - consequence_term_ids=[26, 29], + consequence_term_ids=[23, 26], is_lof_nagnag=None, lof_filter_ids=None, ), @@ -220,7 +221,7 @@ def test_sorted_transcript_consequences_38( mane_select='NM_015658.4', mane_plus_clinical=None, biotype_id=39, - consequence_term_ids=[12], + consequence_term_ids=[9], exon=hl.Struct(index=15, total=19), intron=None, alphamissense=hl.Struct(pathogenicity=0.10000000149011612), @@ -251,7 +252,7 @@ def test_sorted_transcript_consequences_38( mane_select=None, mane_plus_clinical=None, biotype_id=38, - consequence_term_ids=[26, 29], + consequence_term_ids=[23, 26], exon=hl.Struct(index=13, total=17), intron=None, alphamissense=hl.Struct(pathogenicity=0.9700000286102295), @@ -282,7 +283,7 @@ def test_sorted_transcript_consequences_38( mane_select=None, mane_plus_clinical=None, biotype_id=38, - consequence_term_ids=[26, 16, 29], + consequence_term_ids=[23, 13, 26], exon=hl.Struct(index=1, total=5), intron=None, alphamissense=hl.Struct(pathogenicity=None), diff --git a/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py b/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py index 3a036af90..996959fcf 100644 --- a/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py +++ b/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py @@ -540,11 +540,11 @@ def test_multiple_update_vat( ht.locus.position <= 878809, # noqa: PLR2004 ).sorted_transcript_consequences.consequence_term_ids.collect(), [ - [[12], [26, 29], [26, 16, 29]], - [[12], [26, 29], [26, 16, 29]], - [[12], [26, 29], [26, 16, 29]], - [[12], [26, 29], [26, 16, 29]], - [[12], [26, 29], [26, 16, 29]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], + [[9], [23, 26], [23, 13, 26]], ], ) self.assertCountEqual( From d2bd8c1f419614e76450e2931a5cf6ea17cb5bc3 Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Wed, 26 Jun 2024 14:04:58 -0400 Subject: [PATCH 2/2] ruff --- v03_pipeline/lib/annotations/snv_indel_test.py | 1 - 1 file changed, 1 deletion(-) diff --git a/v03_pipeline/lib/annotations/snv_indel_test.py b/v03_pipeline/lib/annotations/snv_indel_test.py index 00b411245..eba8541a6 100644 --- a/v03_pipeline/lib/annotations/snv_indel_test.py +++ b/v03_pipeline/lib/annotations/snv_indel_test.py @@ -119,7 +119,6 @@ def test_sorted_transcript_consequences_37( ht, ), ) - print(ht.sorted_transcript_consequences.collect()) self.assertCountEqual( ht.sorted_transcript_consequences.collect(), [